rs12962411

Variant names:

• chr18-31811560-G-A
• rs12962411

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.071 in 152,202 control chromosomes in the GnomAD database, including 401 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.071 (401 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10804 AN: 152084 Hom.: 402 Cov.: 32

Gnomad AFR AF: 0.0578

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0546

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.0723

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.0791

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0710 AC: 10807 AN: 152202 Hom.: 401 Cov.: 32 AF XY: 0.0704 AC XY: 5242 AN XY: 74430

African (AFR) AF: 0.0578 AC: 2402 AN: 41532

American (AMR) AF: 0.0640 AC: 978 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 508 AN: 3468

East Asian (EAS) AF: 0.0545 AC: 282 AN: 5172

South Asian (SAS) AF: 0.0841 AC: 405 AN: 4818

European-Finnish (FIN) AF: 0.0723 AC: 767 AN: 10608

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0762 AC: 5181 AN: 68008

Other (OTH) AF: 0.0787 AC: 166 AN: 2108

Alfa AF: 0.0786 Hom.: 991

Bravo AF: 0.0708

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.77
PhyloP100		0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12962411; hg19: chr18-29391523;